VMD comes with several useful plugins which can be used without VMD - catdcd and cionize just to name the two which made me wonder where the plugins have gone. The plugins are honored by the ebuild but it fails to build the plugins without any notification! 1) The current ebuild should at least fail, when a plugin could not be build 2) The current ebuild should link/install the plugins into ${PATH} 3) A "plugin" useflag or useflags for each plugin which is not mandatory should be introduced (maybe for the next release of VMD?) Cheers, Bjoern Reproducible: Always Steps to Reproduce: cd /usr/portage/sci-chemistry/vmd ebuild vmd-1.9.ebuild compile Actual Results: Fails to compile plugins! For example: mkdir -p ../compile/lib_LINUX/bin/catdcd4.0 x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./hash.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/hash.o x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -Isrc -I../molfile_plugin/src -c src/psfres.C -fPIC -o../compile/lib_LINUX/tcl/autopsf1.3/psfres.o x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -Isrc -I../molfile_plugin/src -c src/psftype.C -fPIC -o../compile/lib_LINUX/tcl/autopsf1.3/psftype.o x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./catdcd.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/catdcd.o make[2]: *** No rule to make target `../compile/lib_LINUX/molfile/libmolfile_plugin.a', needed by `../compile/lib_LINUX/bin/catdcd4.0/catdcd'. Stop. make[2]: *** Waiting for unfinished jobs.... x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -Isrc -I../molfile_plugin/src -c src/psftypelist.C -fPIC -o../compile/lib_LINUX/tcl/autopsf1.3/psftypelist.o ./catdcd.c:17:31: fatal error: libmolfile_plugin.h: No such file or directory compilation terminated. make[2]: *** [../compile/lib_LINUX/bin/catdcd4.0/catdcd.o] Error 1 Expected Results: Should compile plugins ;-) Portage 2.2.0_alpha30 (default/linux/amd64/10.0, gcc-4.5.2, libc-0-r0, 2.6.38.4-unpatched x86_64) ================================================================= System uname: Linux-2.6.38.4-unpatched-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.2 Timestamp of tree: Tue, 26 Apr 2011 11:45:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 4.1_p9 dev-java/java-config: 1.3.7-r1, 2.1.11-r3 dev-lang/python: 2.6.6-r2, 2.7.1-r1, 3.1.3-r1 dev-util/ccache: 2.4-r9 dev-util/cmake: 2.8.4 sys-apps/baselayout: 2.0.2 sys-apps/openrc: 0.8.2 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 sys-kernel/linux-headers: 2.6.36.1 virtual/os-headers: 0 Repositories: gentoo private-repo Installed sets: @system ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /usr/share/themes/oxygen-gtk/gtk-2.0" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--jobs=4" FEATURES="assume-digests binpkg-logs ccache distlocks fixlafiles fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox" FFLAGS="" GENTOO_MIRRORS="ftp://de-mirror.org/distro/gentoo/ ftp://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.belnet.be/mirror/rsync.gentoo.org/gentoo/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de en en_US sv" MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/private" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="64bit X a52 aac aalib accessibility acct ace acl additions aften aiglx akonadi alias alisp alsa amd64 apbs archive ares asf aspell ass assistant audio autodock bash-completion berkdb bittorrent blast bluetooth branding bwscheduler bzip2 cairo cdaudio cdda cddb cdio cdparanoia cdr cealign chm clamav clucene colorama connectionstatus consolekit contrast cpudetection cracklib crypt css cuda cups cupsddk curl cvs cxx daap dbus device-mapper dga divscore divx4linux djbfft djvu dnotify downloadorder dri drm dts dv dvd dvdnav dvdr dvdread dynmap editor edl embedded emerald emovie emovix enblend enca encode eselect excel exceptions exif extensions extras faac faad fam fbcon ffmpeg fftw flac fltk fontconfig foomaticdb fortran fpx ftp fts3 gcj gdbm gecko gif gimp gimpprint git glib glitz glsl gnuplot gnutls gpg gpm gps graphviz grub gs gstreamer gtk hdri helicheck highlight history hpcups hpijs hunspell icons iconv icotools icu idb imagemagick infowidget inotify ipfilter irc irda jabber java jbig jpeg jpeg2k kde kde4 kdehiddenvisibility kdrive kipi kontact kross kvm lame lapack lastfm lcms libsamplerate lirc live lm_sensors logitech-mouse logrotate logviewer lua lzma lzo mad madwifi matroska mediaplayer melt metalink midi mjpeg mkl mmap mmx mmxext mng modplug mp3 mp4 mpeg mplayer msms mudflap multilib musepack musicbrainz mysql nas ncurses netapi netpbm network network-cron networking networkmanager new-hpcups nfs nls normalize nptlonly nsplugin ntfs numpy nvidia offensive ogg openal openexr opengl openmp oscar osdmenu otr pam parted pcre pda pdf perl phonon pixmaps plasma player plotutils plugins plugins-symlink png policykit povray ppds privacy promol ps pulseaudio python qalculate qmmm-tinker qt-faststart qt3support qt4 quicktime raptor rar raw rdp readline redland rendering resicolor rss rtc rtools samba sasl scanfolder scanner schroedinger script sdk sdl search semantic-desktop sensord shaders sharedmem shm shutdown sift smartcard smbclient smp sndfile solver sox speex spell sql sqlite srt sse sse2 sse3 ssh ssl ssse3 stats subversion svg sysfs tachyon tcltk templates texteffect tga theora threads threadsafe tiff tinker tk toolame traits transcode transparency tremor truetype twolame umfpack unicode urlpicpreview usb userlocales utempter utils v4l v4l2 vcd vditool vdpau vidcap video virtuoso vmd vnc vorbis vpx wav wavpack webdav-neon webinterface webkit wifi winetools wireshark wmf wmp wxwindows x264 xcb xcomposite xembed xine xinerama xml xmp xorg xorgmodule xpdf-headers xprint xv xvid xvmc zip zlib" ALSA_CARDS="sbxfi hda-intel intel8x0" ALSA_PCM_PLUGINS="adpcm dmix linear rate shm softvol extplug plug ioplug hooks empty asym" CAMERAS="canon" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LINGUAS="de en en_US sv" LIRC_DEVICES="asusdh" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" SANE_BACKENDS="umax" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 271297 [details] vmd-1.9-compile.log # grep -n Error vmd-1.9-compile.log 570:make[2]: *** [../compile/lib_LINUX/bin/catdcd4.0/catdcd.o] Error 1 605:make[2]: *** [../compile/lib_LINUX/bin/cionize1.0/getplugins.o] Error 1 616:make[2]: *** [../compile/lib_LINUX/bin/cionize1.0/cionize_molfileio.o] Error 1 620:make[2]: *** [../compile/lib_LINUX/bin/cionize1.0/cionize_internals.o] Error 1 1241:make[2]: *** [../compile/lib_LINUX/tcl/volutil1.3/getplugins.o] Error 1 Cheers, Bjoern
Perhaps you could provide an initial patch for the ebuild.
Lets see who is faster, but my schedule doesn't look that good :-( Since I am not into the building process of VMD/Plugins I will not try to fix this, but see if I can ramp up the ebuild to include a useflag for the plugins as soon as the major bug has been fixed. Cheers, Bjoern
Hmpf, I can't figure out why libmolfile_plugin.h is missing when the lib is called molfile_plugin.h It's here /var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/include/molfile_plugin.h but gcc invoked from portage looks for libmolfile_plugin.h. Portage: emake TCLINC=-I/usr/include TCLLIB=-L/usr/lib64 NETCDFLIB=-L/usr/lib64 NETCDFINC=-I/usr/include NETCDFLDFLAGS=-lnetcdf LINUX [...] make[2]: Entering directory `/var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/catdcd' mkdir -p ../compile/lib_LINUX/bin/catdcd4.0 x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./hash.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/hash.o x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./catdcd.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/catdcd.o ./catdcd.c:17:31: fatal error: libmolfile_plugin.h: No such file or directory compilation terminated. make[2]: *** [../compile/lib_LINUX/bin/catdcd4.0/catdcd.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/catdcd' Manual (in /var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/): make TCLINC=-I/usr/include TCLLIB=-L/usr/lib64 NETCDFLIB=-L/usr/lib64 NETCDFINC=-I/usr/include NETCDFLDFLAGS=-lnetcdf LINUX [...] make[2]: Entering directory `/var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/catdcd' mkdir -p ../compile/lib_LINUX/bin/catdcd4.0 x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./hash.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/hash.o x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./catdcd.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/catdcd.o make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/catdcd' [...] To reproduce the portage compile process I ran the following steps: # ebuild vmd-1.9-r1.ebuild prepare # cd /var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/ # make TCLINC=-I/usr/include TCLLIB=-L/usr/lib64 NETCDFLIB=-L/usr/lib64 NETCDFINC=-I/usr/include NETCDFLDFLAGS=-lnetcdf LINUX [...] make[2]: Entering directory `/var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/catdcd' mkdir -p ../compile/lib_LINUX/bin/catdcd4.0 x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./hash.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/hash.o x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -I. -I../include -I../compile/lib_LINUX/molfile -c ./catdcd.c -fPIC -o../compile/lib_LINUX/bin/catdcd4.0/catdcd.o make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/vmd-1.9-r1/work/plugins/catdcd' [...] This works perfectly... no Errors here. I am just using catdcd as an example since this is the first to fail. Others depending on molfile_plugin.h fail the same way. Any ideas? Cheers, Bjoern
+ 10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild: + Remove USE=static-libs beacuse this breaks build, #365051 +
